[BioC] GoHyperG

[Robert Gentleman]

If what you want is the mapping from some manufacturer's identifiers to  
gene symbols (?) then
you need to use the data packages (if you are using affy then you get  
the one for your chip, if not, then you have more work to do, but you  
didn't really give us very much to go on here)

So, for example, if I had some affy ids from a HG-U95a2 chip, in a  
vector x,
I would do something like

library(hgu95av2)
mysyms = unlist(mget(x, hgu95av2SYMBOL))

if what you want is to first, find all genes that have a GO annotation,  
given a chip you can use
the mappings in hgu95av2GO2PROBE or hgu95av2GO2ALLPROBES (and I will  
leave it to you to read the manual pages and find out what the  
difference is)
eg.
 > hgu95av2GO2ALLPROBES$"GO:0000022"
        TAS
"37171_at"

and then
  > hgu95av2SYMBOL$"37171_at"
[1] "KIF23"

Robert

On Feb 24, 2005, at 6:53 AM, Katleen De Preter wrote:

> Dear colleagues,
> I have a little question about managing data from the GoHyperG  
> function.
> I would like to obtain a table with the 20 most significant  BP-GO  
> terms of a genelist (obtained with SAM), the p-values, the discription  
> of the GO term and a column with the gene-names (comma-separated) from  
> the genelist that belong to these GO terms. How can I obtain this last  
> column???
>
> I managed to obtain the 3 first columns with:
> GOtest<-GOHyperG(genelist,what="BP")
> table<-data.frame(sort(GOtest$pvalues)[1:t],GOtest$intCounts[1: 
> t],goterms[rownames(as.matrix(GOtest$intCounts[1:t]))])
>
> Thank you in advance!
> Katleen De Preter
>
>
>
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| Robert Gentleman              phone: (206) 667-7700                    
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| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
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| Fred Hutchinson Cancer Research Center                                 
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| email: rgentlem at fhcrc.org                                              
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